Dcm2Dcm StreamUtils.skipFully() EOFException

[qq1045561395]

version:dcm4che5.29.0

I want to compress my dicom.

The code is as follows.

        ByteArrayInputStream byteArrayInputStream = new ByteArrayInputStream(buffer);
        try (Transcoder transcoder = new Transcoder(new DicomInputStream(byteArrayInputStream))) {
            transcoder.setIncludeFileMetaInformation(true);
            transcoder.setRetainFileMetaInformation(false);
            transcoder.setEncodingOptions(DicomEncodingOptions.DEFAULT);
            // jpeg2000
            transcoder.setDestinationTransferSyntax(UID.JPEG2000Lossless);
            if (TransferSyntaxType.JPEG_2000.isPixeldataEncapsulated()) {
                transcoder.setCompressParams(params.toArray(new Property[params.size()]));
            }
            ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();

            transcoder.transcode(new Transcoder.Handler() {
                @Override
                public OutputStream newOutputStream(Transcoder transcoder1, Attributes dataset) throws IOException {
                    return byteArrayOutputStream;
                }
            });
            byte[] bytes = byteArrayOutputStream.toByteArray();
            FileOutputStream fileOutputStream = new FileOutputStream(dest);
            fileOutputStream.write(bytes);
            fileOutputStream.close();
        } catch (Exception e) {
            throw e;
        }

Throw anomaly.

16:58:28.676 [main] DEBUG org.dcm4che3.imageio.codec.Transcoder - Compressor: org.dcm4che3.opencv.NativeJ2kImageWriter
16:58:28.834 [main] DEBUG org.dcm4che3.imageio.codec.Transcoder - Compressed frame #1 in 136 ms, ratio 33.67608:1
Failed to transcode C:\Users\Administrator\Desktop\test\1.dcm: null
java.io.EOFException
	at org.dcm4che3.util.StreamUtils.skipFully(StreamUtils.java:78)
	at org.dcm4che3.io.DicomInputStream.skipFully(DicomInputStream.java:469)
	at org.dcm4che3.imageio.codec.Transcoder.compressPixelData(Transcoder.java:596)
	at org.dcm4che3.imageio.codec.Transcoder.processPixelData(Transcoder.java:513)
	at org.dcm4che3.imageio.codec.Transcoder.access$800(Transcoder.java:71)
	at org.dcm4che3.imageio.codec.Transcoder$1.readValue(Transcoder.java:466)
	at org.dcm4che3.io.DicomInputStream.readAttributes(DicomInputStream.java:681)
	at org.dcm4che3.io.DicomInputStream.readAllAttributes(DicomInputStream.java:568)
	at org.dcm4che3.imageio.codec.Transcoder.transcode(Transcoder.java:440)
	at org.dcm4che3.tool.dcm2dcm.Dcm2Dcm.transcodeWithTranscoder(Dcm2Dcm.java:428)
	at org.dcm4che3.tool.dcm2dcm.Dcm2Dcm.transcode(Dcm2Dcm.java:343)
	at org.dcm4che3.tool.dcm2dcm.Dcm2Dcm.mtranscode(Dcm2Dcm.java:334)
	at org.dcm4che3.tool.dcm2dcm.Dcm2Dcm.mtranscode(Dcm2Dcm.java:316)
	at org.dcm4che3.tool.dcm2dcm.Dcm2Dcm.main(Dcm2Dcm.java:288)

Although this solves the problem, I only have a byte array
Transcoder transcoder = new Transcoder(new DicomInputStream(byteArrayInputStream))
Modify as follows
Transcoder transcoder = new Transcoder(new DicomInputStream(new File("c:\\test.dcm")))

[qq1045561395]

dis.length() is 7515424 and imageDescriptor.getLength() is 7515423,so the padding result is equal to 1.

   private void compressPixelData() throws IOException {
        int padding = dis.length() - imageDescriptor.getLength();
        for (int i = 0; i < imageDescriptor.getFrames(); i++) {
            if (decompressor == null){
                readFrame();
            }
            else{
                decompressFrame(i);
            }

            if (i == 0) {
                extractEmbeddedOverlays();
                adjustDataset();
                writeDataset();
                dos.writeHeader(Tag.PixelData, VR.OB, -1);
                dos.writeHeader(Tag.Item, null, 0);
            }
            nullifyUnusedBits();
            bi = palette2rgb ? BufferedImageUtils.convertPalettetoRGB(originalBi, bi)
                    : ybr2rgb ? BufferedImageUtils.convertYBRtoRGB(originalBi, bi)
                    : imageDescriptor.is16BitsAllocated8BitsStored()
                    ? BufferedImageUtils.convertShortsToBytes(originalBi, bi) // workaround for JPEG codec issue
                    : originalBi;
            compressFrame(i);
        }
        dis.skipFully(padding);

        dos.writeHeader(Tag.SequenceDelimitationItem, null, 0);
    }

At this step, count is 0 and in.read() is -1, resulting in an error message.

public static void skipFully(InputStream in, long n) throws IOException {
        while (n > 0) {
            long count = in.skip(n);
            if (count == 0) {
                if (in.read() == -1) {
                    throw new EOFException();
                }
                count = 1;
            }
            n -= count;
        }
    }

Modify as follows.in.skip(n) is 1,Can be successfully executed
Transcoder transcoder = new Transcoder(new DicomInputStream(new File("c:\\test.dcm")))